A Real-time quantitative PCR assay to quantify the Toxoplasma gondii apicoplast was studied. Primers were designed to amplify a 305bp product specific to T. gondii apicoplast. Standard curves were generated for both T. gondii apicoplast DNA and genomic DNA, and were used to compute the relative concentration of apicoplast DNA copies in the test samples. The results indicated that the copies of T. gondii apicoplast DNA was significantly low when exposed to ciprofloxacin, clindamycin and azithromycin for 48h in the second infectious cycle. Our study shows that the Real-time PCR technique is a simple and quick technique for screening the anti-apicoplast drugs.